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DNA barcoding of Gobiid fishes (Perciformes: Gobiidae) from eastern and northeastern India with new record of a Gobionellinae species for the region

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Boni Amin Laskar at Zoological Survey of India
Boni Amin Laskar
Vikas Kumar at Zoological Survey of India
Vikas Kumar
Shantanu Kundu at Pukyong National University
Shantanu Kundu
Kaomud Tyagi at Zoological Survey of India
Kaomud Tyagi
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Abstract

The study attempted identification of Gobiid fishes from freshwaters in the east and northeast India on a collection of 20 specimens. The DNA barcode data delineated the collected samples into three species clades in the neighbor-joining tree. The results confirmed the identification of five sample sequences belonging to the subfamily Gobionellinae due to cohesive cladding with Awaous congeners. This is a new subfamily record for the northeastern region. Another 15 sample sequences showed conspecific cladding with Glossogobius giuris in the database. Among the 15 sample sequences, 14 sequences cladded with G. giuris sequences of Indian specimens while one sample sequence cladded with G. giuris sequences of South African specimens. This indicated the presence of either a hidden species or a previously synonymized species in the G. giuris complex.
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Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
ISSN: 2470-1394 (Print) 2470-1408 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn21
DNA barcoding of Gobiid fishes (Perciformes:
Gobiidae) from eastern and northeastern India
with new record of a Gobionellinae species for the
region
Boni Amin Laskar, Vikas Kumar, Shantanu Kundu, Kaomud Tyagi, Devkant
Singha, Rajasree Chakraborty, Sumantika Chatterjee & Soumitra Saha
To cite this article: Boni Amin Laskar, Vikas Kumar, Shantanu Kundu, Kaomud Tyagi, Devkant
Singha, Rajasree Chakraborty, Sumantika Chatterjee & Soumitra Saha (2016): DNA barcoding of
Gobiid fishes (Perciformes: Gobiidae) from eastern and northeastern India with new record of
a Gobionellinae species for the region, Mitochondrial DNA Part A
To link to this article: http://dx.doi.org/10.3109/24701394.2016.1143470
Published online: 25 Feb 2016.
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MITOCHONDRIAL DNA, 2016
http://dx.doi.org/10.3109/24701394.2016.1143470
SHORT COMMUNICATION
DNA barcoding of Gobiid fishes (Perciformes: Gobiidae) from eastern and
northeastern India with new record of a Gobionellinae species for the region
Boni Amin Laskar, Vikas Kumar, Shantanu Kundu, Kaomud Tyagi, Devkant Singha, Rajasree Chakraborty,
Sumantika Chatterjee and Soumitra Saha
Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata, India
ABSTRACT
The study attempted identification of Gobiid fishes from freshwaters in the east and northeast India
on a collection of 20 specimens. The DNA barcode data delineated the collected samples into three
species clades in the neighbor-joining tree. The results confirmed the identification of five sample
sequences belonging to the subfamily Gobionellinae due to cohesive cladding with Awaous
congeners. This is a new subfamily record for the northeastern region. Another 15 sample
sequences showed conspecific cladding with Glossogobius giuris in the database. Among the 15
sample sequences, 14 sequences cladded with G. giuris sequences of Indian specimens while one
sample sequence cladded with G. giuris sequences of South African specimens. This indicated the
presence of either a hidden species or a previously synonymized species in the G. giuris complex.
ARTICLE HISTORY
Received 13 October 2015
Revised 4 January 2016
Accepted 14 January 2016
Published online
15 February 2016
KEYWORDS
Awaous; Chindwin basin;
Glossogobius; Goby fish;
Kaladan basin; mitochondrial
COI
Introduction
The family Gobiidae of the order Perciformes (Class:
Actinopterygii) is the most speciose of marine fishes and is
also well represented in brackish and freshwater habitats
(Mohlmann & Randall 2002) with nearly 2000 extant species
currently recognized (Agorreta et al. 2013; Viswambharan et al.
2015). Gobiid fishes are mainly characterized by having ventral
fins united into one below the pectorals (Hamilton 1822). The
classification of the family gobiidae has been revised from time
to time with the evidence from molecular data. The phylogen-
etic assessment also includes the discovery of many new
species in the family (Agorreta et al. 2013). At the present time,
there are as many as 34 species of gobiid fishes inhabiting in
Indian region including marine, estuaries, deltas, freshwater
and islands (Froese & Pauly 2015).
Hamilton (1822) had classified 12 species of the genus
Gobius from the Ganga drainage in eastern India that are
currently classified into three subfamilies, viz., Oxudercinae
(seven species), Gobiinae (one species) and Gobionellinae
(three species) (Eschmeyer 2015). Hamilton could survey very
limited areas of the northeastern India. As of late, McClelland
(1839) surveyed the northeastern region and followed by other
workers during the last three decades. At the present time,
Glossogobius giuris (Hamilton 1822) belonging to the subfamily
Goniinae is the only freshwater fish species of the family
Gobiidae recorded from the entire northeastern India (Goswami
et al. 2012). This species is primarily freshwater living but often
migrates to sea due to the amphidromous nature. However, in
the taxonomic history, a gobius of Hamilton’s description viz.,
Gobius gutum has been synonymized with Gobius (current
name Glossogobius)giuris (Kottelat 2013). Hamilton recorded
that G. giuris grows to large size and attains a length of almost a
foot while compared to G. gutum. Thus, it appears that the
synonymy of G. gutum and G. giuris is uncertain. The northeast
India represents a vast locality comprising of three principal
river basins, viz., the Brahmaputra, the Barak and the Kaladan.
Hitherto, no specific survey targeting the gobiid fishes inhabit-
ing in the freshwater ecosystems in northeast India is available.
We investigated the freshwater gobiid fishes inhabiting across
the major river systems in the eastern and northeastern India to
understand the diversity of gobiids as well as the genetic
variations among the population in distant river basins
extending from Chindwin to Ganga. We employed the widely
used DNA barcoding technique for species level identification
that has emerged as a powerful tool in the inventorying of
earth’s biota (Hebert et al. 2003). The technique complements
the traditional taxonomy in identifying taxa by quickly
comparing with the global database. Thereby, the technique
allows easy and fastest insight in differentiating taxa bearing
indiscernible morphological differences. We utilized the agreed
upon barcode segment of cytochrome c oxidase subunit 1
mitochondrial region (mtCOI) to assess the species composition
and genetic diversity within the family Gobiidae from the east
and northeast India.
Materials and methods
Fish specimens were collected from rivers flowing into the
Indian territory of the Chindwin basin, the Ganga basin and the
Kaladan basin and were identified following the recognized
morphological descriptions (Talwar & Jhingran 1991).
CONTACT Vikas Kumar vikaszsi77@gmail.com Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India (ZSI), Kolkata 700053, India
ß2016 Taylor & Francis
Downloaded by [New York University] at 11:10 05 March 2016
The sampling was done from outside of any protected area
jurisdiction, hence no sampling regulation exists. Fishes were
tagged with sampling ID to preserve in 70% ethyl alcohol for
downstream morphological and molecular studies. DNA extrac-
tion, PCR amplification and purification of PCR products were
performed as per our previous studies (Laskar et al. 2013).
Sequencing was performed bi-directionally at Zoological
Survey of India’s in-house sequencing facility (Kundu et al.
2015).
The homology search was done using Basic Local Alignment
Search Tool search in GenBank database. Some of the
congeneric and conspecific sequences of the same or related
taxa were retrieved from NCBI database and aligned theme
with the sample sequences by using the Clustal X program
(Thompson et al. 1997). The mean genetic divergences were
calculated using Kimura 2 parameter (K2P) in MEGA6.0 (Tamura
et al. 2013). Cladistic analysis was performed on K2P parameter
under the optimality criteria of neighbor-joining (NJ) by using
MEGA6.0 with 1000 bootstrap support. Accession numbers, as
well as the respective voucher numbers of the sequences used
in the dataset, are available in the phylogenetic tree where the
sample sequences are marked.
Results and discussion
Based on the DNA barcode data, our sample sequences
showed the closest similarity with the database sequences of
the species within the family Gobiidae. It is important to note
here that the northeast India is reported to be inhabited by
only single species (G. giuris) within the family Gobiidae
(Goswami et al. 2012). However, our sample sequences
formed three distinct species clades due to 18.7–26.3% K2P
genetic distance among them (Table 1). A clade of five sample
sequences (accession number KT364554–KT364558) having
0.02% within group K2P distance showed highest similarity
(93%) with Awaous congeners. The K2P distance of these five
sample sequences with the Awaous congeners were from 9.9%
to 12% (Table 1). The genus Awaous belongs to the subfamily
Gobionellinae of the family Gobiidae. Thus, the identification of
these five sample sequences was confirmative up to sub
familial level only. Phylogenetic tree constructed by Barcode of
Life Database (BOLD) workbench revealed cladding of these
five sample sequences within the congeneric clade of Awaous
while the genus Stiphodon positioned as the out-group. The
genus Stiphodon also belongs to the order Perciformes of
family Gobiidae and subfamily Gobionellinae. The partial mtCOI
data of sample sequences (n¼5) from Kaladan river basin
showed congeneric cladding with Awaous aneofuscus and
Awaous ocellaris in NJ tree (Figure 1). At the stage, in the
absence of DNA barcode data on all the extant species of the
subfamily Gobionellinae, the identification of our sample
sequences was inconclusive beyond subfamily level. The
study evidenced the existence of a Gobionellinae species in
the freshwater in northeast India which is a new record of the
subfamily for the region. The Gobionellinae fish specimens
were collected from the Kaladan drainage in south Mizoram
that flows into the Bay of Bengal through Myanmar. The
Kaladan basin is less explored for fish species composition as
compared to other drainages in northeast India. Nevertheless,
the identification of the Gobionellinae fish up to species level is
urgent and requires further sampling.
Another 15 sample sequences showed highest similarity
(99%) with G. giuris in the database. In the database, there are,
however, two sets of sequences being tagged by the same
name (G. giuris). A set of G. giuris from India and another set of
G. giuris from South Africa. Among the sample sequences of G.
giuris, one sequence (voucher no. ZSI G189, accession number
KT364543) collected from river Ganges showed only 1.4%
genetic divergence with the South African sequences of G.
giuris. The South African clade of G. giuris showed 0.02%
intraspecific genetic divergence. The sequences of Indian clade
of G. giuris in the database along with the 14 sample sequences
(accession number KT364539–KT364542, KT364544–KT364553)
from Chindwin and Ganga basin were conspecific due to low
nucleotide divergence of maximum 0.08% within group K2P
distance while they were distinct from the South African clade
of G. giuris by 12.3–13.1% K2P genetic distance (Table 1). The
interspecific genetic distance between Glossogobius congeners
showed that the Indian G. giuris is close to the G. ankaranensis
due to 11.1% K2P distance than to the South African G. giuris by
12.3–13.1% K2P distance. The six studied Glossogobius con-
geners showed 11.1–25% genetic divergence among each
other. The particular sample specimen (ZSI G189) that cladded
with the South African G. giuris sequences was morphologically
also different from the other 14 sample specimens with regard
to the height of ventral fin and height of caudal fin. The height
of ventral fin was 73.65% in ZSI G189 specimen while it was
65.69–66.4% in other G. giuris specimens. The height of caudal
Table 1. K2P genetic distance of Glossogobius and Awaous species in studied dataset to reflect high genetic divergence between sample sequences of G. giuris as well
as database sequences.
Taxa K2P distance
G. giuris_Indian clade & sample
G. ankaranensis 0.111
G. giuris_South African clade 0.123 0.148
G. giuris_sample (ZSI G189) 0.131 0.152 0.014
G. aureus 0.153 0.143 0.140 0.137
G. callidus 0.183 0.199 0.171 0.177 0.168
G. circumpectus 0.184 0.189 0.210 0.212 0.201 0.219
G. olivaceus 0.206 0.206 0.228 0.230 0.222 0.240 0.025
Awaous_sp. database 0.231 0.245 0.215 0.220 0.237 0.250 0.186 0.201
Awaous sp. sample (Kaladan River) 0.241 0.228 0.191 0.192 0.211 0.237 0.205 0.228 0.101
A. aeneofuscus 0.247 0.263 0.207 0.213 0.230 0.241 0.205 0.230 0.094 0.099
A. ocellaris 0.257 0.260 0.213 0.213 0.233 0.255 0.208 0.226 0.101 0.120 0.105
Further, sample sequences of Awaous sp. from Kaladan River showed high divergence from available sequences of Awaous congeners in the database.
2B. A. LASKAR ET AL.
Downloaded by [New York University] at 11:10 05 March 2016
fin was 90.05% in ZSI G189 specimen while it was 78.79–79.16%
in other G. giuris specimens (cladded with Indian G. giuris). The
ventral fin and caudal fin height were greatly higher in percent
of head length in the particular sample specimen that cladded
with the South African G. giuris. This indicated that the two
clades of G. giuris are actually different species (Figure 1).
Although, most of the morphology are alike in the studied
specimens of both the clades, but the differences in fin height
appeared to be significant enough to consider them different
species. In the taxonomic history, G. gutum has been con-
sidered as a synonym of G. giuris (Kottelat 2013). We assumed
that G. gutum may be a distinct species from G. giuris that
JX983307
JX260874
ZSI G27_KT364541_Chindwin River
ZSI G202_KT364552_Gangetic River
ZSI G196_KT364547_Gangetic River
JX983309
JX983304
ZSI G25_KT364539_Chindwin River
ZSI G26_KT364540_Chindwin River
ZSI G28_KT364542_Chindwin River
ZSI G203_KT364553_Gangetic River
ZSI G198_KT364548_Gangetic River
ZSI G199_KT364549_Gangetic River
ZSI G201_KT364551_Gangetic River
JX260876
ZSI G192_KT364545_Gangetic River
ZSI G194_KT364546_Gangetic River
ZSI G200_KT364550_Gangetic River
JX260875
KF646581
KF646580
KF646579
KF646578
KF646577
KF646576
ZSI G190_KT364544_Gangetic River
G. giuris_India
G. ankaranensis
JQ619668
G. giuris_Gangetic River
ZSI G189_KT364543
JF493543
JF493540
JF493542
JF493539
G. giuris_South Africa
KC789534
EF609360
KC789535
KJ202163
KJ202164
EF607394
KJ669470
G. aureus
JF493534
JF493533
JF493535
JQ619669
HQ945956
JF493536
JF493538
JF493537
G. callidus
NC 018824
JX536695 G. circumpectus
NC 016664
JQ001860 G. olivaceus
ZSI G73_KT364554
ZSI G77_KT364558
ZSI G74_KT364555
ZSI G76_KT364557
ZSI G75_KT364556
Awaous sp._Kaladan River
Awaous sp.
KF668869
A. ocellaris
JX983227
HQ945921
HQ945950
HQ945930
HQ945923
A. aeneofuscus
97
62
100
72
47
64
100
100
84
100
38
68
100
100
60
54
100
81
100
22
70
100
100
90
100
45
98
71
94 95
100
64
26
64
17
48
44
31
17
17
39
0.02
ZSI G190
ZSI G189
ZSI G74
Figure 1. Neighbor-joining tree delimits two clades of barcode sequences of South African and India specimens tagged by G. giuris in the database. One of the studied
sample sequence marked by black square cladded with South African G. giuris while the rest of 14 sample sequences marked by black dots cladded with Indian
G. giuris. The tree further reflects a distinct clade of five sample sequences marked by black dyes that cladded as a congener of Awaous belonging to the subfamily
Gobionellinae. Illustrated image of the representative sample with voucher number in each clade is provided with the respective clade.
MITOCHONDRIAL DNA 3
Downloaded by [New York University] at 11:10 05 March 2016
warrants further study with more samples. The study thereby
evidenced that either is a hidden or a previously synonymized
species actually contained in the G. giuris complex.
Acknowledgements
The authors thank Director, Zoological Survey of India for providing
necessary facilities.
Disclosure statement
The authors declare no conflicts of interest in any form related to this work.
Funding information
Funding support for this work was provided by DST-SERB Young Scientist
project (SB/FT/LS-162/2012) to BA, DBT Post-Doctoral Fellowship to SK and
the core funding of Zoological Survey of India, Kolkata. The funders had no
role in study design, data collection and analysis or preparation of the
manuscript.
References
Agorreta A, San Mauro D, Schliewen U, Van Tassell JL, Kovac
ˇic
´M, Zardoya R,
Ru¨ ber L. 2013. Molecular phylogenetics of Gobioidei and phylogenetic
placement of European gobies. Mol Phylogenet Evol. 69:619–633.
Eschmeyer WN. 2015. Catalog of Fishes, California Academy of Sciences;
[cited 2015 Jun 22] Available at: http://research.calacademy.org/
research/ichthyology/catalog/fishcatmain.asp
Froese R, Pauly D. 2015. FishBase. World Wide Web electronic publication;
[cited 2015 Aug] Available at: www.fishbase.org
Goswami UC, Basistha SK, Bora D, Shyamkumar K, Saikia B, Changsan K.
2012. Fish diversity of North East India, inclusive of the Himalayan and
Indo Burma biodiversity hotspots zones: a checklist on their taxonomic
status, economic importance, geographical distribution, present status
and prevailing threats. Int J Biodivers Conserv. 4:592–613.
Hamilton F. 1822. An account of the fishes found in the River Ganges and its
branches. Edinburgh: Archibald Constable and Company 405.
Hebert PD, Cywinska A, Ball SL, deWaard JR. 2003. Biological identifications
through DNA barcodes. Proc Biol Sci. 270:313–322.
Kottelat M. 2013. The fishes of the inland waters of southeast
Asia: a catalogue and core bibliography of the fishes known
to occur in freshwaters, mangroves and estuaries. Raff Bull
Zool. 27:1–663.
Kundu S, Laskar BA, Venkataraman K, Banerjee D, Kumar V. 2015. DNA
barcoding of Nilssonia congeners corroborates existence of wild N.
nigricans in northeast India. Mitochondrial DNA. Informa healthcare,
DOI:10.3109/19401736.2015.1046176.
Laskar BA, Bhattacharjee MJ, Dhar B, Mahadani P, Kundu S, Ghosh SK.
2013. The species dilemma of Northeast Indian Mahseer
(Actinopterygii: Cyprinidae): DNA barcoding in clarifying the riddle.
PLoS One. 8:e53704.
McClelland J. 1839. Indian Cyprinidae. Asiatic Researches. Calcutta: Bishop
College Press.
Mohlmann MS, Randall JE. 2002. Three new species of gobiid fishes of the
genus Amblyeleotris from the central and western pacific. Raff Bull Zool.
50:215–226.
Talwar PK, Jhingran A. 1991. Inland fishes of India and adjacent countries.
New Delhi: Oxford and IBH Publishing.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6:
Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol.
30:2725–2729.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The
CLUSTAL_X windows interface: Flexible strategies for multiple sequence
alignment aided by quality analysis tools. Nucleic Acids Res.
25:4876–4882.
Viswambharan D, Pavan-Kumar A, Singh DP, Jaiswar AK, Chakraborty SK,
Nair JR, Lakra WS. 2015. DNA barcoding of gobiid fishes (Perciformes,
Gobiodei). Mitochondrial DNA. 26:15–9.
4B. A. LASKAR ET AL.
Downloaded by [New York University] at 11:10 05 March 2016
... According to Kottelat (2013) the genus name Giuris is masculine in gender, and therefore the correct nomenclature is Giuris margaritaceus, the current organism name in the NCBI GenBank and BOLD nucleotide sequence databases. 46 Within the Gobioidei, cryptic and morphologically similar species can complicate identification based on external morphology, [46][47][48][49] and there have been many taxonomic revisions in the Gobiidae, including the Family Eleotridae. There are at least 10 "non valid" synonyms of G. margaritacea Valenciennes 1837 (originally Eleotris margaritacea Valenciennes 1837) listed in FishBase, including Ophieleotris aporos (originally Eleotris aporos Bleeker 1854) and junior synonyms under the genera Eleotris (n=7), Hypseleotris (n=1), and Ophieleotris (n=1). ...
... The deep divisions within the putative G. margaritaceus clade in Figure 3 are similar to the deep divisions in Glossogobius giuris from India. 49 A study on the ichthyofauna of Java and Bali 88 reported two BOLD BINs for Giuris margaritacea from this region, with a genetic distance of 12.56%, indicating more than one species in this region of Indonesia. Recent studies on the genus Giuris within the Indonesian Archipelago 15 It is interesting that no Giuris sequence from Indonesia were closely related to the payangka from Bolano Sau Lake (Figure 4), and evolutionary relationships within Giuris do not necessarily seem to follow readily discernable patterns based on past or present geographical distance. ...
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... The deep divisions within the putative G. margaritaceus clade in Figure 3 are similar to the deep divisions in Glossogobius giuris from India. 49 It is interesting that no Giuris sequence from Indonesia were closely related to the payangka from Bolano Sau Lake (Figure 4), and evolutionary relationships within Giuris do not necessarily seem to follow readily discernible patterns based on past or present geographical distance. For example, as in Ref. 53, Australian and Philippine clades (the latter including payangka from Bolano Sao Lake) seem more closely related to each other than to species found in areas lying between these two regions ( Figure 4; Table 2), with one of the two barcoded lacustrine Giuris populations from the northern arm of Sulawesi (Bolano Sau and Tondano) belonging to each of these clades. ...
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Full-text available
  • Jan 2023
Background : The freshwater ichthyofauna of Wallacea is diverse and understudied. A baseline survey of Bolano Sau Lake in Parigi Moutong District, Central Sulawesi Province, Indonesia in 2019 found an eleotrid goby (local name payangka) with characters conforming to the genus Giuris , long considered monophyletic as G. margaritacea/G. margaritaceus but recently found to comprise at least eight species. This study focused on the molecular (DNA barcoding) identification and phenotypic characters of the payangka. Methods : Payangka samples were collected from August to December 2019 in collaboration with local fishermen, weighed and measured, and preserved in 75% ethanol. Length, weight, sex (n=111) and 17 morphometric characters/six meristic counts (n=42) were recorded. DNA barcoding was performed on a fin clipping preserved in 96% ethanol. Homologous nucleotide sequences were obtained from public (GenBank and BOLD) databases, analysis conducted in MEGA X, and phylogenetic trees edited in the Interactive Tree of Life (iToL). Results : Within the deeply divided Giuris clade, the payangka sequence resolved into a sub-clade identified as Giuris laglaizei (Sauvage 1880), a recently resurrected taxon, based on a sequence provided by Philippe Keith. The length-weight relationship (L = 0.0087∙W3.162) indicated mildly allometric positive growth. Size distribution differed significantly between male and female fish with significantly larger mean size of males (13.56 cm) than females (11.62 cm). The meristic formula was: D VI-I,8 A I,8 P 13 V I,5 C15. Phylogenetic analysis indicated four Giuris species in wetlands around Tomini Bay and five in Sulawesi. Conclusions : This first record of G. laglaizei in Indonesia advances knowledge of Wallacean and Indo-Pacific Gobiiformes biogeography and highlights the need for a revision of the conservation status of the taxa currently grouped under Giuris margaritacea/G. margaritaceus in the IUCN Red List and FishBase databases. The data will inform biodiversity and fisheries management at local and regional levels.
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... There is morphological support for the observed genetic differentiation between clusters. For example, Laskar et al. (2016) noted that their G. giuris specimen with GenBank accession no. KT364543 that belongs to G. giuris 2 cluster, was morphologically different from other G. giuris specimens (KT364539, KT364541, KT364544, KT364547, KT364549, KT364552-53) that are grouped in the G. giuris 3 cluster. ...
DNA barcoding of Glossogobius species (Teleostei: Gobiidae) from major lakes in the Philippines reveals the presence of cryptic species and species complexes
Article
Full-text available
  • Jul 2022
Glossogobius is the most speciose among all the genera of the family Gobiidae. Eight species of Glossogobius have been reported in the Philippines, which include the most abundant and commercially important species, G. aureus. In this study, Glossogobius specimens were collected from nine lakes in the Philippines. A total of 113 specimens were DNA barcoded using the mitochondrial cytochrome c oxidase subunit I (COI) gene. Additional sequences of Glossogobius were mined from GenBank. The neighbor-joining (NJ) tree showed that all the specimens from Laguna de Bay, Naujan, Buluan, Bato, Buhi, and Paoay lakes clustered with G. aureus sequences from GenBank with a 99% bootstrap support. Ten of the 14 specimens from Taal Lake were also included in this cluster; the other four specimens morphologically identified as G. illimis formed a separate cluster. The specimens from Lake Lanao formed two separate groups: one group clustered with G. aureus, while the other group formed a separate cluster and were designated as G. cf. aureus because they are morphologically similar to G. aureus, but are genetically divergent from it. All the 20 specimens from Lake Mainit formed a separate cluster and are most likely a new and still undescribed species. DNA barcoding also lends support to previous studies which showed, based on morphological data, that G. giuris and G. celebius are species complexes. Within-species genetic distances suggest that G. callidus, G. bicirrhosus, and G. circumspectus are also species complexes. The discovery of possibly new species from Lake Mainit, cryptic species from Lake Lanao, and the presence of species complexes in Glossogobius have implications on the proper conservation and management of these important fishery resources.
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... COI gene is the best resolution of the intraspecific level than other core genes (Bellagamba et al. 2015;Hubert et al. 2015;Rodrigues et al. 2017;Bingpeng et al. 2018;Roesma et al. 2018, Yulianto et al. 2020). In addition, mitochondrial COI genes are also widely and reliably utilized to identify species in the goby group (Jeon et al. 2012;Viswambharan et al. 2013;Laskar et al. 2016;Lejeune et al. 2016;Wang et al. 2017;Linh et al. 2018;Olii et al. 2019;Sahami et al. 2019a;Sahami et al. 2019b;Pasisingi et al. 2020b;Roesma et al. 2020;. Following the protocol kit, 20 grams of fish meat tissue of a new variant individual was isolated using Qiagen Tissue and blood extraction kits for genetic analysis. ...
Diversity of species in making up Nike fish schools and a new record of Eleotris melanosoma in Tomini Paguyaman Bay, Gorontalo, Indonesia
Article
Full-text available
  • Nov 2021
Sahami FM, Habibie SA. 2021. Diversity of species in making up Nike fish schools and a new record of Eleotris melanosoma in Tomini Paguyaman Bay, Gorontalo, Indonesia. Biodiversitas 22: 5459-5467. Several estuaries in the waters of Tomini Bay are reported as the primary location for Nike fishing in Gorontalo; one of which is Paguyaman Bay. However, scientific information on Nike fish in the Tomini Bay waters is currently limited in Gorontalo Bay. The present study aims to determine the diversity of species in making up the Nike fish schools in Paguyaman Bay and show the types of constituent species whose distribution in Gorontalo waters has never been reported. A total of 1773 samples of Nike fish were collected from the sea to the estuary of Paguyaman Bay in one period of their emergence on April 8-10, 2021. The species were grouped based on the melanophore pattern’s similarity and then analyzed morphometrically. The molecular identification of COI mitochondrial DNA was performed on species with different morphological appearances from those found in Gorontalo Bay. The Discriminant Function Analysis (DFA) indicated that the main distinguishing character of morphometrics is body depth. The morphological results suggested that the Nike fish schools in Paguyaman Bay consisted of seven species, four genera, and two families, i.e., Sicyopterus longifilis, S. parvei, S. cynocephalus, Stiphodon semoni, Belobranchus segura, B. belobranchus, and Eleotris melanosoma. The first finding of E. melanosoma as a species making up the Nike fish schools in Paguyaman Bay was a new variant of the distribution of this species in Gorontalo waters and confirmed using morphology and molecular analysis. Further, based on the species composition, Nike fish schools in the waters of Paguyaman Bay show a typical species dominance trend during the recruitment process returning to freshwater, i.e., S. longifilis (52%) on the first day, Belobranchus segura (63.27%) on the second day, and Stiphodon semoni (83.43%) on the third day.
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... The classification of the family Gobiidae has been revised from time to time with the evidence from molecular data (Laskar et al., 2017). A. ocellaris is one of the species of the Gobiidae family, which is scientifically recorded generally as a species inhabiting Indo-Pacific waters. ...
Are Awaous ocellaris and Belobranchus belobranchus the two species of Nike fish schools ?
Article
Full-text available
  • Jun 2020
Investigating goby fish is vital to perform an integrated and comprehensive study in order to maintain the roles of the fish, thus providing balanced ecosystem functions and services, as well as contributing to fish biodiversity. Local societies simply recognize fish species by their local names, which are not common. This condition, in turn, causes hitches in conducting further studies. Nike, the name of a local fish, refers to the schools of goby fish larvae whose adult phase has not been fully confirmed. This study aimed to reveal the species that categorizes as nike fish through tracing adult goby inhabiting freshwater. Two fish samples, i.e., Unknown 01 and Unknown 02, were taken from two sites in Bone River, Gorontalo, Indonesia. These samples were captured purposively using a hand net by considering the morphological similarity between the two target samples and the general characteristic of goby. Furthermore, the samples were analyzed genetically through the PCR sequencing method using the Mitochondrial Cytochrome Oxidase Subunit 1 (CO1) gene. Based on the NCBI database, Unknown 01 had the highest similarity to Belobranchus belobranchus (99.54%), while Unknown 02 was identical with Awaous ocellaris (100%). Unknown 01 and Unknown 02, compared to the BOLD database, the similarity level, had the highest percentage of similarity with B. belobranchus (99.85%) and A. ocellaris (100%), respectively. Therefore, A. ocellaris and B. belobranchus were strongly alleged as two species making up the goby schools in the adult stadia that reach freshwater during their migration.
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... Nonetheless, specific names that can be applied to giuris A and giuris B require further broader investigation of type material and available names. A recent proliferation of regional F I G U R E 5 Field identification tool box for the large-growing Glossogobius of northern Australia, including visual key, character matrix and tips on character recognition (see also Akihito &Meguro, 1975, andAllen, 2012, for more detailed drawings of papillae patterns) Table 1 and Tables S1 and S2 barcode initiatives (e.g., Abdulmalik-Labe & Quilang, 2019; Ahmed, 2017;Dahruddin et al., 2017;Laskar et al., 2017;Patil et al., 2018;Thu et al., 2019;Wang et al., 2018) greatly contributes to a collective international data pool (Ratnasingham & Hebert, 2007), suggesting much broader distributions for both species and that G. giuris s.l. likely pertains to a complex of at least four species ( giuris A-D). ...
Unravelling the taxonomy and identification of a problematic group of benthic fishes from tropical rivers (Gobiidae: Glossogobius)
Article
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Flathead gobies (genus Glossogobius) include c. 40 small‐ to medium‐sized benthic fishes found primarily in freshwater habitats across the Indo‐Pacific, having biodiversity value as well as cultural and economic value as food fishes, especially in developing countries. To help resolve considerable confusion regarding the identification of some of the larger‐growing Glossogobius species, a systematic framework was established using nuclear genetic markers, mitochondrial DNA barcoding and phenotypic evidence for a geographically widespread collection of individuals from the waterways of tropical northern Australia. Species boundaries and distribution patterns were discordant with those previously reported, most notably for the tank goby Glossogobius giuris, which included a cryptic species. Genetic divergence was matched with accompanying unique visual characters that aid field identification. Additional taxonomic complexity was also evident, by comparison with DNA barcodes from international locations, suggesting that the specific names applicable for two of the candidate species in Australia remain unresolved due to confusion surrounding type specimens. Although flathead gobies are assumed to be widespread and common, this study demonstrates that unrealised taxonomic and ecological complexity is evident, and this will influence assessments of tropical biodiversity and species conservation. This study supports the need for taxonomic studies of freshwater fishes to underpin management in areas subject to significant environmental change.
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The first record of the olive flathead gudgeon, Butis gymnopomus (Bleeker, 1853) (Gobiiformes: Butidae), from Kerala, India
Article
Full-text available
  • Mar 2025
The small gobioid fishes of the family Butidae, commonly known as "gudgeons" or "sleepers," inhabit tropical freshwater and brackishwaters across the Indo-Pacific region. Of the ten recognized species in the diverse genus Butis Bleeker, six are reported from India’s marine and inland habitats. Despite extensive surveys, only two species, B. butis and B. koilomatodon, have been documented in Kerala. This study confirms the identity of the little-known gudgeons of the genus Butis in Vembanad-Kole, a Ramsar site in Kerala, India, using morphological and molecular analyses. Additionally, it records the first occurrence of Butis gymnopomus on India’s west coast. These results stress the ecological importance of the Vembanad-Kole wetlands and contribute to regional fish biodiversity better.
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DNA barcoding of waterbirds: A novel technique in environmental conservation biology
Article
Full-text available
  • Dec 2021
Cytochrome c oxidase I (COI) is one of the mitochondrial genes, an excellent marker used for the DNA barcoding of various organisms. The COI was isolated from twelve different species of waterbirds using the Gene Elute DNA miniprep Kit. The relationship among the waterbirds was assessed by making a phylogenetic tree with the software MEGA-X. The phylogenetic tree's dendrogram showed two main branches in which seven species of water birds aligned one group with four subgroups and the remaining five species aligned with two subgroups based on their similar COI sequences. The Little egret showed 96% similarity with the Cattle egret, Purple heron and Oriental Darter produced 94% similarity with the Grey heron, pond heron shared 90% similarity with the Black-crowned night heron, Asian openbill shared 89% with Pheasant-tailed Jacana and the Common coot 94% similarity with White-breasted waterhen. The pond heron and the Black-crowned night heron showed zero % pairwise distance, but the Cattle egret, Little egret, Oriental Darter, Purple heron and Grey heron showed <0.29%. However, the other seven species of water birds showed >12% of the pairwise distance. Twenty-one conserved haplotypes have been shown in their COI sequences based on the multiple sequences alignment. DNA barcoding identifies the species with their genetic property rather than based on their ecology and behvaviour.
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Biological identification through DNA barcodes
Article
Full-text available
  • Jan 2003
Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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The fishes of the inland waters of Southeast Asia: A catalogue and core bibliography of the fishes known to occur in freshwaters, mangroves and estuaries
Article
Full-text available
  • Nov 2013
  • RAFFLES B ZOOL
There are 3108 valid and named native fish species in the inland waters of Southeast Asia between the Irrawaddy and Red River drainages, the small coastal drainages between the Red River and Hainan, the whole Indochinese Peninsula, Andaman and Nicobar Islands, Indonesia (excluding Papua Province, Waigeo, Aru [but Kai is included]), and the Philippines. They belong to 137 families. Their taxonomy and nomenclature are reviewed. The original descriptions of all 7047 recorded species-group names and 1980 genus-group names have been checked in the original works for correct spelling, types, type locality and bibliographic references. The bibliography includes about 4700 titles. Synonymies are given, based on published information as well as unpublished observations. The names of 49 introduced species and 347 extralimital taxa cited in the discussions have also been checked. The original descriptions of all species not present in the covered area but cited as type species of genera have been checked for availability, authorship, date and correct spelling. The availability of some family-group names has been checked when there was suspicion of possible nomenclatural problems. Bibliographic notes include new informations on the dates of publication of works by, among others, Bleeker, Bloch, Heckel and Steindachner and discussion of authorship of names in various works.
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MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0
Article
Full-text available
  • Oct 2013
  • MOL BIOL EVOL
We announce the release of an advanced version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis. In version 6.0, MEGA now enables the inference of timetrees, as it implements our RelTime method for estimating divergence times for all branching points in a phylogeny. A new Timetree Wizard in MEGA6 facilitates this timetree inference by providing a graphical user interface (GUI) to specify the phylogeny and calibration constraints step-by-step. This version also contains enhanced algorithms to search for the optimal trees under evolutionary criteria and implements a more advanced memory management that can double the size of sequence data sets to which MEGA can be applied. Both GUI and command-line versions of MEGA6 can be downloaded from www.megasoftware.net free of charge.
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DNA barcoding of gobiid fishes (Perciformes, Gobioidei)
Article
Full-text available
  • Sep 2013
  • MITOCHONDR DNA
Abstract Gobiids constitute a major proportion of fish population in both tropical and temperate freshwater as well as marine ecosystem. Due to their small size, cryptic ecology and ambiguous morphological characters, gobiids diversity was not documented completely. In this study, DNA barcodes were generated for 11 species of gobiids, collected from the Ashtamudi Lake, India. The mitochondrial COI gene was amplified using universal primers and the resulted 650 bp amplicon was sequenced. The COI barcodes clearly distinguished all the species with high inter-specific genetic distance values than intra-specific values based on K2P (Kimura 2 Parameter) model. The average genetic distance (K2P model) within species, genus and family was 1.2%, 22.2% and 25.3%, respectively. In addition to barcode-based species identification system, Nucleotide Diagnostic (ND) characters specific for species were identified. The Neighbor-Joining tree revealed distinct clusters shared by the species of same genera.
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Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies
Article
Full-text available
  • Jul 2013
Gobioidei is one of the largest suborders of teleost fishes, with nearly 2000 extant species currently recognized. They have a worldwide distribution and show a spectacular variety in morphology, ecology, and behavior. Despite their importance, phylogenetic relationships among many groups of gobioids (including some of the major lineages) still remain poorly understood. In this study, we analyze sequence data of five molecular markers (two mitochondrial and three nuclear) averaging 6000 bp for 222 species of gobioids. Our study is the first to include both multiple nuclear and mitochondrial genes to reconstruct a comprehensive multilocus phylogeny of gobioids encompassing most major lineages representing the overall diversity of one of the most speciose vertebrate lineages. Two separate datasets are produced and used to specifically address the phylogenetic placement of Rhyacichthyidae and Odontobutidae, and the phylogenetic relationships among gobioid lineages. Our results strongly support that the initial split in the gobioid tree separated a clade containing Rhyacichthyidae + Odontobutidae as the sister group of all other lineages. The family Eleotrididae branches off the gobioid tree after the Rhyacichthyidae + Odontobutidae clade, followed by the Butidae as sister to the Gobiidae. Additionally, several major monophyletic groups are confidently identified within the two major Gobiidae subclades, the gobiine-like gobiids and the gobionelline-like gobiids. Robustness of the phylogenetic trees inferred here is significantly higher than that of previous studies, hence our results provide the most compelling molecular phylogenetic hypothesis of Gobioidei thus far. For the first time, we provide a comprehensive sampling of European gobies that traditionally have been divided into "transverse" and "sand gobies". We show that the European gobies cluster in three distinct lineages, the Pomatoschistus-, Aphia-, and Gobius-lineages. The former resolved within the gobionelline-like gobiids and the latter two within the gobiine-like gobiids. These findings have significant implications for our understanding of the phylogeographic origin of European gobies in the light of the closure of the Paratethys. A rogue taxon analysis identified Kraemeria as an unstable taxon decreasing support at the base of the gobiine-like gobiids. Removal of this rogue taxon significantly increased phylogenetic resolution in that part of the tree and revealed additional insights into early bursts of cladogenesis of the gobiine-like gobiids.
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Three new species of gobiid fishes of the genus Amblyeleotris from the Central and Western Pacific
Article
Full-text available
  • Jun 2002
  • RAFFLES B ZOOL
ABSTRAC7: -Three new species of the Indo-Pacific goby genus Amblyeleotris are described from the central and western Pacific. The species of this genus live symbiotically with alpheid shrimps, and all are colored with bars that vary from dark brown to red, orange, or yellow. Amblyeleotris rubrimarginata from the Great Barrier Reef and New Caledonia has 13 (rarely 14) dorsal soft rays, 14 (rarely IS) anal soft rays, 77-94 scales in longitudinal series, pelvic fins united for about 10% of their length, pelvic frenum present, a dark spot behind the eye, and a red margin or rows of small red spots on the dorsal and caudal fins. Amblyeleotris harrisorum from Kiritimati (Christmas Island), Line Islands, has 13 dorsal soft rays, 14 anal soft rays, 81- 96 scales in longitudinal series, pelvic fins separate, no pelvic frenum, a bright yellow caudal fin, and oblique yellow lines behind the eye. Amblyeleotris marquesas from Nuku Hiva, Marquesas Islands has 14 dorsal soft rays, IS anal soft rays, 92-96 scales in longitudinal series, pelvic fins united for about 10% of their length, no pelvic frenum, broad orangish brown bars with a narrow bar in upper half of each white interspace.
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DNA barcoding of Nilssonia congeners corroborates existence of wild N. nigricans in northeast India
Article
  • Jun 2015
  • MITOCHONDR DNA
DNA barcode data of soft-shell turtles is limited in global DNA database while it is completely lacking for the highly debated species Nilssonia nigricans. We employed DNA barcoding technique to discriminate the species cluster for Nilssonia congeners, especially for the highly debated N. nigricans from different localities of northeast India. Sampling across the region included a few live specimens from wild, market sold carcass specimens, and a few dry carapaces meant for home decoration purpose. The generated sequences (621 bp of mtCOI) of dry carapaces showed 99-100% homology with the generated sequences of morphologically identified N. nigricans. The COI barcode sequences of N. nigricans (n = 12) showed 3.8% mean genetic divergence with N. hurum (n = 3), 10% with N. gangetica (n = 4), and 9.2% with N. formosa (GenBank sequences). Similarly, the mtCytb sequences of the dry carapace and live specimens of N. nigricans were 99-100% homologous with the conspecific database sequences and formed specific clusters. The inferred Neighbor-Joining (NJ), Maximum Likelihood (ML), and Bayesian (BA) phylogeny based on partial mtCOI gene efficiently discriminated all the congeners of Nilssonia into specific clusters and, therefore, it was helpful to detect the existence of N. nigricans.
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